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Rodrigues Jardim B, Gambley C, Tran-Nguyen LTT, Webster C, Kehoe M, Kinoti WM, Bond S, Davis R, Jones L, Pathania N, Sharman M, Chapman T, Rodoni BC, Constable FE. A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions. Microb Genom 2024; 10:001213. [PMID: 38446015 PMCID: PMC10999746 DOI: 10.1099/mgen.0.001213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group ('Ca. Phytoplasma stylosanthis'; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and 'Ca. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of 'Ca. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | | | - Craig Webster
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Monica Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Samantha Bond
- Biosecurity and Animal Welfare, Department of Industry, Tourism and Trade, Darwin, Northern Territory, Australia
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Nandita Pathania
- Department of Agriculture and Fisheries, Mareeba, Queensland, Australia
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Toni Chapman
- Biosecurity and Food Safety, New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, 2567, Australia
| | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
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Wang R, Bai B, Li D, Wang J, Huang W, Wu Y, Zhao L. Phytoplasma: A plant pathogen that cannot be ignored in agricultural production-Research progress and outlook. MOLECULAR PLANT PATHOLOGY 2024; 25:e13437. [PMID: 38393681 PMCID: PMC10887288 DOI: 10.1111/mpp.13437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024]
Abstract
Phytoplasmas are phloem-restricted plant-pathogenic bacteria transmitted by insects. They cause diseases in a wide range of host plants, resulting in significant economic and ecological losses worldwide. Research on phytoplasmas has a long history, with significant progress being made in the past 30 years. Notably, with the rapid development of phytoplasma research, scientists have identified the primary agents involved in phytoplasma transmission, established classification and detection systems for phytoplasmas, and 243 genomes have been sequenced and assembled completely or to draft quality. Multiple possible phytoplasma effectors have been investigated, elucidating the molecular mechanisms by which phytoplasmas manipulate their hosts. This review summarizes recent advances in phytoplasma research, including identification techniques, host range studies, whole- or draft-genome sequencing, effector pathogenesis and disease control methods. Additionally, future research directions in the field of phytoplasma research are discussed.
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Affiliation(s)
- Ruotong Wang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Bixin Bai
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Danyang Li
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Jingke Wang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Weijie Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Yunfeng Wu
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Lei Zhao
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
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3
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Maluta N, Castro T, Spotti Lopes JR. DC-electrical penetration graph waveforms for Dalbulus maidis (Hemiptera: Cicadellidae) and the effects of entomopathogenic fungi on its probing behavior. Sci Rep 2023; 13:22033. [PMID: 38086916 PMCID: PMC10716247 DOI: 10.1038/s41598-023-48779-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The corn leafhopper Dalbulus maidis is an important transmitter of viruses and bacteria to maize plants. Data on the stylet probing and ingestion behavior of D. maidis, gathered using the DC-electrical penetration graph (DC-EPG) technique, are limited. The increasing prevalence of this pest and the diseases that it transmits in maize crops heighten the importance of studying how control tools affect the probing behavior of these insects, to reduce or prevent the chances of pathogen transmission and the damage from feeding. Our study recorded stylet activities of D. maidis, using a DC-EPG system and compared the appearances of waveforms with those from published AC and AC-DC EPG studies. All types of systems produced similar waveform appearances; therefore, we used the waveform nomenclature previously published. We also determined the effects of the entomopathogenic fungus Cordyceps javanica on the probing behavior of D. maidis at different time points after the fungus was applied by spraying. Forty-eight hours after the insects were sprayed, the effects were pronounced, with significant disruption of the stylet activities in phloem and non-phloem phases. Our study indicated that this commercial microbiological product, with the active ingredient C. javanica, can alter the probing behavior of D. maidis and may be helpful in management of the vector.
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Affiliation(s)
- Nathalie Maluta
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, C.P. 9, Piracicaba, SP, 13418-900, Brazil.
- Koppert Biological Systems, Rodovia Margarida da Graça Martins s/n - Km 17.5, Piracicaba, SP, 13400-970, Brazil.
| | - Thiago Castro
- Koppert Biological Systems, Rodovia Margarida da Graça Martins s/n - Km 17.5, Piracicaba, SP, 13400-970, Brazil
| | - João Roberto Spotti Lopes
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, C.P. 9, Piracicaba, SP, 13418-900, Brazil
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Xue C, Zhang Y, Li H, Liu Z, Gao W, Liu M, Wang H, Liu P, Zhao J. The genome of Candidatus phytoplasma ziziphi provides insights into their biological characteristics. BMC PLANT BIOLOGY 2023; 23:251. [PMID: 37173622 PMCID: PMC10176825 DOI: 10.1186/s12870-023-04243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Phytoplasmas are obligate cell wall-less prokaryotic bacteria that primarily multiply in plant phloem tissue. Jujube witches' broom (JWB) associated with phytoplasma is a destructive disease of jujube (Ziziphus jujuba Mill.). Here we report the complete 'Candidatus Phytoplasma ziziphi' chromosome of strain Hebei-2018, which is a circular genome of 764,108-base pairs with 735 predicted CDS. Notably, extra 19,825 bp (from 621,995 to 641,819 bp) compared to the previously reported one complements the genes involved in glycolysis, such as pdhA, pdhB, pdhC, pdhD, ackA, pduL and LDH. The synonymous codon usage bias (CUB) patterns by using comparative genomics analysis among the 9 phytoplasmas were similar for most codons. The ENc-GC3s analysis among the 9 phytoplasmas showed a greater effect under the selection on the CUBs of phytoplasmas genes than mutation and other factors. The genome exhibited a strongly reduced ability in metabolic synthesis, while the genes encoding transporter systems were well developed. The genes involved in sec-dependent protein translocation system were also identified.The expressions of nine FtsHs encoding membrane associated ATP-dependent Zn proteases and Mn-SodA with redox capacity in the Ca. P. ziziphi was positively correlated with the phytoplasma concentration. Taken together, the genome will not only expand the number of phytoplasma species and provide some new information about Ca. P. ziziphi, but also contribute to exploring its pathogenic mechanism.
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Affiliation(s)
- Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Hongtai Li
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Ping Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071000, China.
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China.
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000, China.
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5
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Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Rodoni B, Constable FE. Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing. Front Microbiol 2022; 13:937648. [PMID: 36033837 PMCID: PMC9411968 DOI: 10.3389/fmicb.2022.937648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Obtaining complete phytoplasma genomes is difficult due to the lack of a culture system for these bacteria. To improve genome assembly, a non-ionic, low- and iso-osmotic iodixanol (Optiprep™) density gradient centrifugation method was developed to enrich for phytoplasma cells and deplete plant host tissues prior to deoxyribonucleic acid (DNA) extraction and high-throughput sequencing (HTS). After density gradient enrichment, potato infected with a ‘Candidatus Phytoplasma australasia’-related strain showed a ∼14-fold increase in phytoplasma HTS reads, with a ∼1.7-fold decrease in host genomic reads compared to the DNA extracted from the same sample without density gradient centrifugation enrichment. Additionally, phytoplasma genome assemblies from libraries equalized to 5 million reads were, on average, ∼15,000 bp larger and more contiguous (N50 ∼14,800 bp larger) than assemblies from the DNA extracted from the infected potato without enrichment. The method was repeated on capsicum infected with Sweet Potato Little Leaf phytoplasma (‘Ca. Phytoplasma australasia’-related strain) with a lower phytoplasma titer than the potato. In capsicum, ∼threefold more phytoplasma reads and ∼twofold less host genomic reads were obtained, with the genome assembly size and N50 values from libraries equalized to 3.4 million reads ∼137,000 and ∼4,000 bp larger, respectively, compared to the DNA extracted from infected capsicum without enrichment. Phytoplasmas from potato and capsicum were both enriched at a density of 1.049–1.058 g/ml. Finally, we present two highly contiguous ‘Ca. Phytoplasma australasia’ phytoplasma reference genomes sequenced from naturally infected Solanaceae hosts in Australia. Obtaining high-quality phytoplasma genomes from naturally infected hosts will improve insights into phytoplasma taxonomy, which will improve their detection and disease management.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora, VIC, Australia
- *Correspondence: Bianca Rodrigues Jardim,
| | | | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries, Maroochy Research Facility, Nambour, QLD, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora, VIC, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora, VIC, Australia
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6
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Wei W, Zhao Y. Phytoplasma Taxonomy: Nomenclature, Classification, and Identification. BIOLOGY 2022; 11:1119. [PMID: 35892975 PMCID: PMC9394401 DOI: 10.3390/biology11081119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of 'Candidatus phytoplasma' species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for 'Candidatus Phytoplasma' species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined.
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Affiliation(s)
- Wei Wei
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA;
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7
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Huang CT, Cho ST, Lin YC, Tan CM, Chiu YC, Yang JY, Kuo CH. Comparative Genome Analysis of ‘Candidatus Phytoplasma luffae’ Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution. Front Microbiol 2022; 13:773608. [PMID: 35300489 PMCID: PMC8923039 DOI: 10.3389/fmicb.2022.773608] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2022] [Indexed: 12/23/2022] Open
Abstract
Phytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has a remarkably repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ∼25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for subfunctionalization or neofunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.
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Affiliation(s)
- Ching-Ting Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Choon-Meng Tan
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ching Chiu
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Jun-Yi Yang,
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Chih-Horng Kuo,
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8
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Tan CM, Lin YC, Li JR, Chien YY, Wang CJ, Chou L, Wang CW, Chiu YC, Kuo CH, Yang JY. Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses. Front Microbiol 2021; 12:766221. [PMID: 34858377 PMCID: PMC8632452 DOI: 10.3389/fmicb.2021.766221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Phytoplasmas are uncultivated plant-pathogenic bacteria with agricultural importance. Those belonging to the 16SrII group, represented by 'Candidatus P. aurantifolia', have a wide range of plant hosts and cause significant yield losses in valuable crops, such as pear, sweet potato, peanut, and soybean. In this study, a method that combines immunoprecipitation-based enrichment and MinION long-read DNA sequencing was developed to solve the challenge of phytoplasma genome studies. This approach produced long reads with high mapping rates and high genomic coverage that can be combined with Illumina reads to produce complete genome assemblies with high accuracy. We applied this method to strain NCHU2014 and determined its complete genome sequence, which consists of one circular chromosome with 635,584 bp and one plasmid with 4,224 bp. Although 'Ca. P. aurantifolia' NCHU2014 has a small chromosome with only 471 protein-coding genes, it contains 33 transporter genes and 27 putative effector genes, which may contribute to obtaining nutrients from hosts and manipulating host developments for their survival and multiplication. Two effectors, the homologs of SAP11 and SAP54/PHYL1 identified in 'Ca. P. aurantifolia' NCHU2014, have the biochemical activities in destabilizing host transcription factors, which can explain the disease symptoms observed in infected plants. Taken together, this study provides the first complete genome available for the 16SrII phytoplasmas and contributes to the understanding of phytoplasma pathogenicity.
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Affiliation(s)
- Choon Meng Tan
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jian-Rong Li
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Yuan-Yu Chien
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Jui Wang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Wei Wang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ching Chiu
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan.,Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan.,Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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9
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Ramos A, Esteves MB, Cortés MTB, Lopes JRS. Maize Bushy Stunt Phytoplasma Favors Its Spread by Changing Host Preference of the Insect Vector. INSECTS 2020; 11:insects11090600. [PMID: 32899467 PMCID: PMC7565095 DOI: 10.3390/insects11090600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/30/2020] [Accepted: 09/03/2020] [Indexed: 01/20/2023]
Abstract
Simple Summary Phytopathogenic bacteria such as phytoplasmas induce physiological changes in their host plants that may modulate the behavior of an insect vector in favor of their own spread. In this study we investigate changes in the host selection behavior of the leafhopper vector, Dalbulus maidis (DeLong and Wolcott), in choice tests between healthy vs. maize bushy stunt phytoplasma (MBSP)-infected maize leaves (Zea mays L.), for insects previously exposed to infected plants (named “bacteriliferous”) or not (naive). The results showed that males and naive females of D. maids did not distinguish the treatments when infected leaves were still asymptomatic, whereas bacteriliferous females prefer to settle on healthy leaves, a behavior that favors pathogen inoculation and primary spread at early crop stages. During the symptomatic phase of maize infection, naive males and females were initially attracted to infected leaves, favoring pathogen acquisition; interestingly, the females tend to move towards healthy leaves a few hours later, a behavioral shift that promotes secondary spread. Overall, this study presents evidences that MBSP optimizes its spread in maize crops by influencing the host selection behavior of the leafhopper vector. Abstract Plant pathogenic bacteria may influence vector behavior by inducing physiological changes in host plants, with implications for their spread. Here, we studied the effects of maize bushy stunt phytoplasma (MBSP) on the host selection behavior of the leafhopper vector, Dalbulus maidis (DeLong and Wolcott). Choice assays contrasting leaves of healthy (mock-inoculated) vs. infected maize (Zea mays L.) were conducted during the asymptomatic and symptomatic phases of plant infection, with leafhopper males or females previously exposed to infected plants (bacteriliferous insects) or not. In each assay, 40 adults were released in choice arenas where only the leaves of two plants from each treatment were offered and visible, and the insects landed on the leaves were counted 1, 2, 3, 5, 7, 9, 11 and 23 h after release. During the asymptomatic phase of plant infection, an effect was observed only on bacteriliferous females, who preferred leaves of healthy plants 5 h after release or later. The symptomatic phase triggered a pull–push effect on non-bacteriliferous females, who were first attracted to symptomatic leaves but hours later moved to healthy leaves. Non-bacteriliferous males initially preferred symptomatic leaves (up to 5 h after release) and later became equally distributed between treatments. Bacteriliferous males and females initially did not discriminate between healthy and symptomatic leaves, but only the females tended to move to healthy leaves 9 h after release. Oviposition was drastically reduced on symptomatic leaves. The changes in vector behavior induced by MBSP favor its primary spread, since bacteriliferous females prefer healthy leaves at early (asymptomatic) stages of the crop. At later stages, secondary spread may be favored because non-bacteriliferous females are initially attracted to infected (symptomatic) leaves, allowing pathogen acquisition and subsequent transmission as they move to healthy plants.
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Affiliation(s)
- Anderson Ramos
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Padua Dias, 11, Piracicaba 13418-900, Brazil
| | - Mariana Bossi Esteves
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Padua Dias, 11, Piracicaba 13418-900, Brazil
| | - Mayerli Tatiana Borbón Cortés
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Padua Dias, 11, Piracicaba 13418-900, Brazil
| | - João Roberto Spotti Lopes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Padua Dias, 11, Piracicaba 13418-900, Brazil
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Cho ST, Kung HJ, Huang W, Hogenhout SA, Kuo CH. Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis. Front Microbiol 2020; 11:1531. [PMID: 32754131 PMCID: PMC7366425 DOI: 10.3389/fmicb.2020.01531] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘Candidatus Phytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share < 94% ANI and < 75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Jui Kung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Jones TKL, Medina RF. Corn Stunt Disease: An Ideal Insect-Microbial-Plant Pathosystem for Comprehensive Studies of Vector-Borne Plant Diseases of Corn. PLANTS 2020; 9:plants9060747. [PMID: 32545891 PMCID: PMC7356856 DOI: 10.3390/plants9060747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 11/16/2022]
Abstract
Over 700 plant diseases identified as vector-borne negatively impact plant health and food security globally. The pest control of vector-borne diseases in agricultural settings is in urgent need of more effective tools. Ongoing research in genetics, molecular biology, physiology, and vector behavior has begun to unravel new insights into the transmission of phytopathogens by their insect vectors. However, the intricate mechanisms involved in phytopathogen transmission for certain pathosystems warrant further investigation. In this review, we propose the corn stunt pathosystem (Zea mays-Spiroplasma kunkelii-Dalbulus maidis) as an ideal model for dissecting the molecular determinants and mechanisms underpinning the persistent transmission of a mollicute by its specialist insect vector to an economically important monocotyledonous crop. Corn stunt is the most important disease of corn in the Americas and the Caribbean, where it causes the severe stunting of corn plants and can result in up to 100% yield loss. A comprehensive study of the corn stunt disease system will pave the way for the discovery of novel molecular targets for genetic pest control targeting either the insect vector or the phytopathogen.
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Affiliation(s)
- Tara-kay L. Jones
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX 77843-2475, USA;
- Texas A&M AgriLife Research—Weslaco, 2415 E. Business 83, Weslaco, TX 78596-8344, USA
| | - Raul F. Medina
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX 77843-2475, USA;
- Correspondence: ; Tel.: +1-979-845-4775
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Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA. Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog 2019; 15:e1008035. [PMID: 31557268 PMCID: PMC6802841 DOI: 10.1371/journal.ppat.1008035] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 10/21/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022] Open
Abstract
Phytoplasmas are insect-transmitted bacterial pathogens that colonize a wide range of plant species, including vegetable and cereal crops, and herbaceous and woody ornamentals. Phytoplasma-infected plants often show dramatic symptoms, including proliferation of shoots (witch's brooms), changes in leaf shapes and production of green sterile flowers (phyllody). Aster Yellows phytoplasma Witches' Broom (AY-WB) infects dicots and its effector, secreted AYWB protein 11 (SAP11), was shown to be responsible for the induction of shoot proliferation and leaf shape changes of plants. SAP11 acts by destabilizing TEOSINTE BRANCHED 1-CYCLOIDEA-PROLIFERATING CELL FACTOR (TCP) transcription factors, particularly the class II TCPs of the CYCLOIDEA/TEOSINTE BRANCHED 1 (CYC/TB1) and CINCINNATA (CIN)-TCP clades. SAP11 homologs are also present in phytoplasmas that cause economic yield losses in monocot crops, such as maize, wheat and coconut. Here we show that a SAP11 homolog of Maize Bushy Stunt Phytoplasma (MBSP), which has a range primarily restricted to maize, destabilizes specifically TB1/CYC TCPs. SAP11MBSP and SAP11AYWB both induce axillary branching and SAP11AYWB also alters leaf development of Arabidopsis thaliana and maize. However, only in maize, SAP11MBSP prevents female inflorescence development, phenocopying maize tb1 lines, whereas SAP11AYWB prevents male inflorescence development and induces feminization of tassels. SAP11AYWB promotes fecundity of the AY-WB leafhopper vector on A. thaliana and modulates the expression of A. thaliana leaf defence response genes that are induced by this leafhopper, in contrast to SAP11MBSP. Neither of the SAP11 effectors promote fecundity of AY-WB and MBSP leafhopper vectors on maize. These data provide evidence that class II TCPs have overlapping but also distinct roles in regulating development and defence in a dicot and a monocot plant species that is likely to shape SAP11 effector evolution depending on the phytoplasma host range.
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Affiliation(s)
- Pascal Pecher
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Gabriele Moro
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Maria Cristina Canale
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, University of São Paulo, Piracicaba, Brazil
| | - Sylvain Capdevielle
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Archana Singh
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Allyson MacLean
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Akiko Sugio
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Joao R. S. Lopes
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, University of São Paulo, Piracicaba, Brazil
| | - Saskia A. Hogenhout
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Cho ST, Lin CP, Kuo CH. Genomic Characterization of the Periwinkle Leaf Yellowing (PLY) Phytoplasmas in Taiwan. Front Microbiol 2019; 10:2194. [PMID: 31608032 PMCID: PMC6761752 DOI: 10.3389/fmicb.2019.02194] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
The periwinkle leaf yellowing (PLY) disease was first reported in Taiwan in 2005. This disease was caused by an uncultivated bacterium in the genus “Candidatus phytoplasma.” In subsequent years, this bacterium was linked to other plant diseases and caused losses in agriculture. For genomic investigation of this bacterium and its relatives, we conducted whole genome sequencing of a PLY phytoplasma from an infected periwinkle collected in Taoyuan. The de novo genome assembly produced eight contigs with a total length of 824,596 bp. The annotation contains 775 protein-coding genes, 63 pseudogenes, 32 tRNA genes, and two sets of rRNA operons. To characterize the genomic diversity across populations, a second strain that infects green onions in Yilan was collected for re-sequencing analysis. Comparison between these two strains identified 337 sequence polymorphisms and 10 structural variations. The metabolic pathway analysis indicated that the PLY phytoplasma genome contains two regions with highly conserved gene composition for carbohydrate metabolism. Intriguingly, each region contains several pseudogenes and the remaining functional genes in these two regions complement each other, suggesting a case of duplication followed by differential gene losses. Comparative analysis with other available phytoplasma genomes indicated that this PLY phytoplasma belongs to the 16SrI-B subgroup in the genus, with “Candidatus Phytoplasma asteris” that causes the onion yellowing (OY) disease in Japan as the closest known relative. For characterized effectors that these bacteria use to manipulate their plant hosts, the PLY phytoplasma has homologs for SAP11, SAP54/PHYL1, and TENGU. For genome structure comparison, we found that potential mobile unit (PMU) insertions may be the main factor that drives genome rearrangements in these bacteria. A total of 10 PMU-like regions were found in the PLY phytoplasma genome. Two of these PMUs were found to harbor one SAP11 homolog each, with one more similar to the 16SrI-B type and the other more similar to the 16SrI-A type, suggesting possible horizontal transfer. Taken together, this work provided a first look into population genomics of the PLY phytoplasmas in Taiwan, as well as identified several evolutionary processes that contributed to the genetic diversification of these plant-pathogenic bacteria.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chan-Pin Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Buoso S, Pagliari L, Musetti R, Martini M, Marroni F, Schmidt W, Santi S. 'Candidatus Phytoplasma solani' interferes with the distribution and uptake of iron in tomato. BMC Genomics 2019; 20:703. [PMID: 31500568 PMCID: PMC6734453 DOI: 10.1186/s12864-019-6062-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/26/2019] [Indexed: 11/25/2022] Open
Abstract
Background ‘Candidatus Phytoplasma solani’ is endemic in Europe and infects a wide range of weeds and cultivated plants. Phytoplasmas are prokaryotic plant pathogens that colonize the sieve elements of their host plant, causing severe alterations in phloem function and impairment of assimilate translocation. Typical symptoms of infected plants include yellowing of leaves or shoots, leaf curling, and general stunting, but the molecular mechanisms underlying most of the reported changes remain largely enigmatic. To infer a possible involvement of Fe in the host-phytoplasma interaction, we investigated the effects of ‘Candidatus Phytoplasma solani’ infection on tomato plants (Solanum lycopersicum cv. Micro-Tom) grown under different Fe regimes. Results Both phytoplasma infection and Fe starvation led to the development of chlorotic leaves and altered thylakoid organization. In infected plants, Fe accumulated in phloem tissue, altering the local distribution of Fe. In infected plants, Fe starvation had additive effects on chlorophyll content and leaf chlorosis, suggesting that the two conditions affected the phenotypic readout via separate routes. To gain insights into the transcriptional response to phytoplasma infection, or Fe deficiency, transcriptome profiling was performed on midrib-enriched leaves. RNA-seq analysis revealed that both stress conditions altered the expression of a large (> 800) subset of common genes involved in photosynthetic light reactions, porphyrin / chlorophyll metabolism, and in flowering control. In Fe-deficient plants, phytoplasma infection perturbed the Fe deficiency response in roots, possibly by interference with the synthesis or transport of a promotive signal transmitted from the leaves to the roots. Conclusions ‘Candidatus Phytoplasma solani’ infection changes the Fe distribution in tomato leaves, affects the photosynthetic machinery and perturbs the orchestration of root-mediated transport processes by compromising shoot-to-root communication. Electronic supplementary material The online version of this article (10.1186/s12864-019-6062-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Buoso
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Laura Pagliari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Rita Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Marta Martini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy.,IGA Technology Services, Via Jacopo Linussio, 51, 33100, Udine, Italy
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, 11529, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, 40227, Taichung, Taiwan
| | - Simonetta Santi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy.
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Multilocus Sequence Analysis Reveals Three Distinct Populations of " Candidatus Phytoplasma palmicola" with a Specific Geographical Distribution on the African Continent. Appl Environ Microbiol 2019; 85:AEM.02716-18. [PMID: 30770404 PMCID: PMC6450020 DOI: 10.1128/aem.02716-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/05/2019] [Indexed: 12/15/2022] Open
Abstract
Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission. To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for “Candidatus Phytoplasma palmicola” based on eight housekeeping genes. At the continental level, eight different sequence types were identified among 132 “Candidatus Phytoplasma palmicola”-infected coconuts collected in Ghana, Nigeria, and Mozambique, where CLYD epidemics are still very active. “Candidatus Phytoplasma palmicola” appeared to be a bacterium that is subject to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, might explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events was found for “Candidatus Phytoplasma palmicola.” The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus “Candidatus Phytoplasma” is underlined. IMPORTANCE Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission.
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Wang N, Yang H, Yin Z, Liu W, Sun L, Wu Y. Phytoplasma effector SWP1 induces witches' broom symptom by destabilizing the TCP transcription factor BRANCHED1. MOLECULAR PLANT PATHOLOGY 2018; 19:2623-2634. [PMID: 30047227 PMCID: PMC6638060 DOI: 10.1111/mpp.12733] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/28/2018] [Accepted: 07/21/2018] [Indexed: 05/18/2023]
Abstract
Phytoplasmas are insect-transmitted phytopathogenic bacteria, which secrete effector proteins that are often responsible for altering the plant morphology and behaviours of their vectors. Phytoplasma multifunctional effector proteins TENGU and SAP11 induce typical witches' broom symptoms, but their mode of action remains unknown. Previously, we have identified a SAP11-like effector from wheat blue dwarf phytoplasma, SWP1, which induces witches' broom symptoms in Nicotiana benthamiana. In this study, we observed that SWP1-expressing transgenic Arabidopsis thaliana plants showed typical witches' broom symptoms. On overexpression of SWP1 truncation mutants in N. benthamiana, we identified that the coiled-coil domain and nuclear localization were responsible for the induction of witches' broom symptoms. In addition, using yeast two-hybrid and bimolecular fluorescence complementation assays, we demonstrated that SWP1 interacts with A. thaliana transcription factor TCP18 (BRC1), the key negative regulator of branching signals in various plant species. Moreover, in planta co-expression analysis showed that SWP1 promotes the degradation of BRC1 via a proteasome system. These findings suggest that the phytoplasma effector SWP1 induces witches' broom symptoms through targeting of BRC1 and promoting its degradation.
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Affiliation(s)
- Nan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
| | - Haizhen Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
| | - Zhiyuan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
| | - Wenting Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYangling712100China
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Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease. BMC Genomics 2018; 19:689. [PMID: 30231900 PMCID: PMC6148798 DOI: 10.1186/s12864-018-5075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement. RESULTS The complete genome sequence of JWB phytoplasma (jwb-nky) was determined, which consisting of one circular chromosome of 750,803 bp with a GC content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31 tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA repeats were identified. Based on PHIbaes analysis, a large number of genes were genome-specific and approximately 13% of JWB phytoplasma genes were predicted to be associated with virulence. Although transporters for maltose, dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine were identified, KEGG pathway analysis revealed the reduced metabolic capabilities of JWB phytoplasma. Comparative genome analyses between JWB phytoplasma and other phytoplasmas shows the occurrence of large-scale gene rearrangements. The low synteny with other phytoplasmas indicated that the expansion of multiple gene families/duplication probably occurred separately after differentiation. CONCLUSIONS In this study, the complete genome sequence of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for the first time and a number of species-specific genes were identified in the genome. The study enhanced our understandings about genomic basis and the pathogenicity mechanism of this pathogen, which will aid in the development of improved strategies for efficient management of JWB diseases.
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Sparks ME, Bottner-Parker KD, Gundersen-Rindal DE, Lee IM. Draft genome sequence of the New Jersey aster yellows strain of 'Candidatus Phytoplasma asteris'. PLoS One 2018; 13:e0192379. [PMID: 29408883 PMCID: PMC5800598 DOI: 10.1371/journal.pone.0192379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/20/2018] [Indexed: 01/21/2023] Open
Abstract
The NJAY (New Jersey aster yellows) strain of ‘Candidatus Phytoplasma asteris’ is a significant plant pathogen responsible for causing severe lettuce yellows in the U.S. state of New Jersey. A draft genome sequence was prepared for this organism. A total of 177,847 reads were assembled into 75 contigs > 518 bp with a total base value of 652,092 and an overall [G+C] content of 27.1%. A total of 733 protein coding genes were identified. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MAPF00000000. This draft genome was used for genome- and gene-based comparative phylogenetic analyses with other phytoplasmas, including the closely related ‘Ca. Phytoplasma asteris’ strain, aster yellows witches’- broom (AY-WB). NJAY and AY-WB exhibit approximately 0.5% dissimilarity at the nucleotide level among their shared genomic segments. Evidence indicated that NJAY harbors four plasmids homologous to those known to encode pathogenicity determinants in AY-WB, as well as a chromosome-encoded mobile unit. Apparent NJAY orthologs to the important AY-WB virulence factors, SAP11 and SAP54, were identified. A number of secreted proteins, both membrane-bound and soluble, were encoded, with many bearing similarity to known AY-WB effector molecules and others representing possible secreted proteins that may be novel to the NJAY lineage.
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Affiliation(s)
- Michael E. Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | | | - Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Ing-Ming Lee
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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Liu J, Gopurenko D, Fletcher MJ, Johnson AC, Gurr GM. Phytoplasmas-The "Crouching Tiger" Threat of Australian Plant Pathology. FRONTIERS IN PLANT SCIENCE 2017; 8:599. [PMID: 28491068 PMCID: PMC5405143 DOI: 10.3389/fpls.2017.00599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Phytoplasmas are insect-vectored bacteria that cause disease in a wide range of plant species. The increasing availability of molecular DNA analyses, expertise and additional methods in recent years has led to a proliferation of discoveries of phytoplasma-plant host associations and in the numbers of taxonomic groupings for phytoplasmas. The widespread use of common names based on the diseases with which they are associated, as well as separate phenetic and taxonomic systems for classifying phytoplasmas based on variation at the 16S rRNA-encoding gene, complicates interpretation of the literature. We explore this issue and related trends through a focus on Australian pathosystems, providing the first comprehensive compilation of information for this continent, covering the phytoplasmas, host plants, vectors and diseases. Of the 33 16Sr groups reported internationally, only groups I, II, III, X, XI and XII have been recorded in Australia and this highlights the need for ongoing biosecurity measures to prevent the introduction of additional pathogen groups. Many of the phytoplasmas reported in Australia have not been sufficiently well studied to assign them to 16Sr groups so it is likely that unrecognized groups and sub-groups are present. Wide host plant ranges are apparent among well studied phytoplasmas, with multiple crop and non-crop species infected by some. Disease management is further complicated by the fact that putative vectors have been identified for few phytoplasmas, especially in Australia. Despite rapid progress in recent years using molecular approaches, phytoplasmas remain the least well studied group of plant pathogens, making them a "crouching tiger" disease threat.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture & Forestry UniversityFuzhou, China
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - David Gopurenko
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
- NSW Department of Primary Industries, Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Murray J. Fletcher
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - Anne C. Johnson
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture & Forestry UniversityFuzhou, China
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
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Miller RNG, Costa Alves GS, Van Sluys MA. Plant immunity: unravelling the complexity of plant responses to biotic stresses. ANNALS OF BOTANY 2017; 119:681-687. [PMID: 28375427 PMCID: PMC5378191 DOI: 10.1093/aob/mcw284] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/16/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants are constantly exposed to evolving pathogens and pests, with crop losses representing a considerable threat to global food security. As pathogen evolution can overcome disease resistance that is conferred by individual plant resistance genes, an enhanced understanding of the plant immune system is necessary for the long-term development of effective disease management strategies. Current research is rapidly advancing our understanding of the plant innate immune system, with this multidisciplinary subject area reflected in the content of the 18 papers in this Special Issue. SCOPE Advances in specific areas of plant innate immunity are highlighted in this issue, with focus on molecular interactions occurring between plant hosts and viruses, bacteria, phytoplasmas, oomycetes, fungi, nematodes and insect pests. We provide a focus on research across multiple areas related to pathogen sensing and plant immune response. Topics covered are categorized as follows: binding proteins in plant immunity; cytokinin phytohormones in plant growth and immunity; plant-virus interactions; plant-phytoplasma interactions; plant-fungus interactions; plant-nematode interactions; plant immunity in Citrus; plant peptides and volatiles; and assimilate dynamics in source/sink metabolism. CONCLUSIONS Although knowledge of the plant immune system remains incomplete, the considerable ongoing scientific progress into pathogen sensing and plant immune response mechanisms suggests far reaching implications for the development of durable disease resistance against pathogens and pests.
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Affiliation(s)
- Robert Neil Gerard Miller
- Universidade de Brasília, Instituto de Ciências Biológicas, 70910-900, Brasilia, DF, Brazil
- For correspondence. Email
| | | | - Marie-Anne Van Sluys
- Universidade de São Paulo, Instituto de Biociências, 05508-090, São Paulo, SP, Brazil
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